There are a few reasons Redump uses split track images. One big one being that computer CD drives have 'read offset' values and add or truncate tracks. Their listings have compensated for all drive variations one track at a time and represent perfect 1:1 copies of the originals. It also helps isolate where a game was changed. Many PS1 games had multiple versions released. Sometimes they include bug fixes, logo changes, or revised audio tracks.
None of those reasons are especially compelling. I honestly suspect they split the tracks mainly as a way to make them smaller for downloading (piracy). Redump itself doesn't support piracy in the slightest that I know of, but such 'perfect copy' databases invariably lead to people hosting pirate copies. Audio and data tracks have different optimal compression methods available, as well as being able to combine identical tracks between multiple releases of the same game.
Anyways, I think all those CUE sheets are showing roughly the same thing. Because Redump's cue sheets expect split files, they don't contain a 'track start' location, just a 'stack order'. Thus, swapping audio tracks should be as easy as changing the name in the cue file to reference the new track. All sizes and LBA stuff is adjusted automatically by the program opening the CUE.
Index00 is where the pregap (blank data leading into an audio track) starts. Index01 is where the actual audio data starts.
The second cue is designed for a 1 piece image and thus lists a track start location in minutes. The first entry lists the the prgap as 'PREGAP' whereas subsequent tracks use 'index 00' - same thing.
Pregaps aren't always detected properly by drives. I've even seen disks that have been mastered incorrectly showing no pre-gap, when they actually do have one. Again, audio data is handled sloppy by a lot of CD drives and dumping programs.
The third cue is also designed for a 1-pice image and appears to have the pre-gaps removed altogether. Its for the edited Rockman, correct? They probably just removed them, or didn't enter them by mistake. As far as I know, the pre-gaps don't serve any purpose on emulated CD drives (aka emulators, virtual drives etc).